DNA extraction and quantification

The DNA was extracted from the specimens using commercially available kits following the manufacturer’s instructions. The best-performing kits based on the biological origin matrix were employed for bacterial DNA extraction. QIAamp DNA Mini Kit (Qiagen, Hilden, Germany) was used to extract exclusively the bacterial DNA (avoiding other microbiome components such as fungi, archaea, and bacteriophages) from sputum, saliva, oral and nasopharyngeal swabs and biopsies, and ZymoBIOMICS DNA Miniprep Kit (Zymo Research, D4300) for vaginal swabs. Then, the DNA concentration and purity were investigated employing a Picodrop microtiter Spectrophotometer (Picodrop, Hinxton, UK).